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MDNorm.cpp
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MDNorm.cpp
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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
// NScD Oak Ridge National Laboratory, European Spallation Source,
// Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidMDAlgorithms/MDNorm.h"
#include "MantidAPI/CommonBinsValidator.h"
#include "MantidAPI/IMDEventWorkspace.h"
#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/Run.h"
#include "MantidAPI/Sample.h"
#include "MantidAPI/SpectrumInfo.h"
#include "MantidDataObjects/MDHistoWorkspace.h"
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidGeometry/Crystal/PointGroupFactory.h"
#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
#include "MantidGeometry/Crystal/SymmetryOperationFactory.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/MDGeometry/HKL.h"
#include "MantidGeometry/MDGeometry/MDFrameFactory.h"
#include "MantidGeometry/MDGeometry/QSample.h"
#include "MantidKernel/ArrayLengthValidator.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/Exception.h"
#include "MantidKernel/Strings.h"
#include "MantidKernel/UnitLabelTypes.h"
#include "MantidKernel/VectorHelper.h"
#include "MantidKernel/VisibleWhenProperty.h"
#include <algorithm>
#include <boost/lexical_cast.hpp>
namespace Mantid::MDAlgorithms {
using namespace Mantid::Kernel;
using namespace Mantid::API;
using namespace Mantid::Geometry;
using namespace Mantid::DataObjects;
namespace {
using VectorDoubleProperty = Kernel::PropertyWithValue<std::vector<double>>;
// function to compare two intersections (h,k,l,Momentum) by Momentum
bool compareMomentum(const std::array<double, 4> &v1, const std::array<double, 4> &v2) { return (v1[3] < v2[3]); }
// k=sqrt(energyToK * E)
constexpr double energyToK = 8.0 * M_PI * M_PI * PhysicalConstants::NeutronMass * PhysicalConstants::meV * 1e-20 /
(PhysicalConstants::h * PhysicalConstants::h);
// compare absolute values of doubles
static bool abs_compare(double a, double b) { return (std::fabs(a) < std::fabs(b)); }
} // namespace
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(MDNorm)
//----------------------------------------------------------------------------------------------
/**
* Constructor
*/
MDNorm::MDNorm()
: m_normWS(), m_inputWS(), m_isRLU(false), m_UB(3, 3, true), m_W(3, 3, true), m_transformation(), m_hX(), m_kX(),
m_lX(), m_eX(), m_hIdx(-1), m_kIdx(-1), m_lIdx(-1), m_eIdx(-1), m_numExptInfos(0), m_Ei(0.0), m_diffraction(true),
m_accumulate(false), m_dEIntegrated(true), m_samplePos(), m_beamDir(), convention("") {}
/// Algorithms name for identification. @see Algorithm::name
const std::string MDNorm::name() const { return "MDNorm"; }
/// Algorithm's version for identification. @see Algorithm::version
int MDNorm::version() const { return 1; }
/// Algorithm's category for identification. @see Algorithm::category
const std::string MDNorm::category() const { return "MDAlgorithms\\Normalisation"; }
/// Algorithm's summary for use in the GUI and help. @see Algorithm::summary
const std::string MDNorm::summary() const {
return "Bins multidimensional data and calculate the normalization on the "
"same grid";
}
//----------------------------------------------------------------------------------------------
/** Initialize the algorithm's properties.
*/
void MDNorm::init() {
declareProperty(
std::make_unique<WorkspaceProperty<API::IMDEventWorkspace>>("InputWorkspace", "", Kernel::Direction::Input),
"An input MDEventWorkspace. Must be in Q_sample frame.");
declareProperty(std::make_unique<WorkspaceProperty<API::IMDEventWorkspace>>(
"BackgroundWorkspace", "", Kernel::Direction::Input, PropertyMode::Optional),
"An (optional) input MDEventWorkspace for background. Must be in Q_lab frame.");
// RLU and settings
declareProperty("RLU", true, "Use reciprocal lattice units. If false, use Q_sample");
setPropertyGroup("RLU", "Q projections RLU");
auto mustBe3D = std::make_shared<Kernel::ArrayLengthValidator<double>>(3);
std::vector<double> Q0(3, 0.), Q1(3, 0), Q2(3, 0);
Q0[0] = 1.;
Q1[1] = 1.;
Q2[2] = 1.;
declareProperty(std::make_unique<ArrayProperty<double>>("QDimension0", Q0, mustBe3D),
"The first Q projection axis - Default is (1,0,0)");
setPropertySettings("QDimension0", std::make_unique<Kernel::VisibleWhenProperty>("RLU", IS_EQUAL_TO, "1"));
setPropertyGroup("QDimension0", "Q projections RLU");
declareProperty(std::make_unique<ArrayProperty<double>>("QDimension1", Q1, mustBe3D),
"The second Q projection axis - Default is (0,1,0)");
setPropertySettings("QDimension1", std::make_unique<Kernel::VisibleWhenProperty>("RLU", IS_EQUAL_TO, "1"));
setPropertyGroup("QDimension1", "Q projections RLU");
declareProperty(std::make_unique<ArrayProperty<double>>("QDimension2", Q2, mustBe3D),
"The thirdtCalculateCover Q projection axis - Default is (0,0,1)");
setPropertySettings("QDimension2", std::make_unique<Kernel::VisibleWhenProperty>("RLU", IS_EQUAL_TO, "1"));
setPropertyGroup("QDimension2", "Q projections RLU");
// vanadium
auto fluxValidator = std::make_shared<CompositeValidator>();
fluxValidator->add<InstrumentValidator>();
fluxValidator->add<CommonBinsValidator>();
auto solidAngleValidator = fluxValidator->clone();
declareProperty(std::make_unique<WorkspaceProperty<>>("SolidAngleWorkspace", "", Direction::Input,
API::PropertyMode::Optional, solidAngleValidator),
"An input workspace containing integrated vanadium "
"(a measure of the solid angle).\n"
"Mandatory for diffraction, optional for direct geometry inelastic");
declareProperty(std::make_unique<WorkspaceProperty<>>("FluxWorkspace", "", Direction::Input,
API::PropertyMode::Optional, fluxValidator),
"An input workspace containing momentum dependent flux.\n"
"Mandatory for diffraction. No effect on direct geometry inelastic");
setPropertyGroup("SolidAngleWorkspace", "Vanadium normalization");
setPropertyGroup("FluxWorkspace", "Vanadium normalization");
// Define slicing
for (std::size_t i = 0; i < 6; i++) {
std::string propName = "Dimension" + Strings::toString(i) + "Name";
std::string propBinning = "Dimension" + Strings::toString(i) + "Binning";
std::string defaultName = "";
if (i < 3) {
defaultName = "QDimension" + Strings::toString(i);
}
declareProperty(std::make_unique<PropertyWithValue<std::string>>(propName, defaultName, Direction::Input),
"Name for the " + Strings::toString(i) + "th dimension. Leave blank for NONE.");
auto atMost3 = std::make_shared<ArrayLengthValidator<double>>(0, 3);
std::vector<double> temp;
declareProperty(std::make_unique<ArrayProperty<double>>(propBinning, temp, atMost3),
"Binning for the " + Strings::toString(i) + "th dimension.\n" +
"- Leave blank for complete integration\n" +
"- One value is interpreted as step\n"
"- Two values are interpreted integration interval\n" +
"- Three values are interpreted as min, step, max");
setPropertyGroup(propName, "Binning");
setPropertyGroup(propBinning, "Binning");
}
// symmetry operations
declareProperty(std::make_unique<PropertyWithValue<std::string>>("SymmetryOperations", "", Direction::Input),
"If specified the symmetry will be applied, "
"can be space group name, point group name, or list "
"individual symmetries.");
// temporary workspaces
declareProperty(std::make_unique<WorkspaceProperty<IMDHistoWorkspace>>("TemporaryDataWorkspace", "", Direction::Input,
PropertyMode::Optional),
"An (optional) input MDHistoWorkspace used to accumulate data from "
"multiple MDEventWorkspaces. If unspecified a blank "
"MDHistoWorkspace will be created.");
declareProperty(std::make_unique<WorkspaceProperty<IMDHistoWorkspace>>("TemporaryNormalizationWorkspace", "",
Direction::Input, PropertyMode::Optional),
"An (optional) input MDHistoWorkspace used to accumulate normalization "
"from multiple MDEventWorkspaces. If unspecified a blank "
"MDHistoWorkspace will be created.");
// temporary background workspace
declareProperty(std::make_unique<WorkspaceProperty<IMDHistoWorkspace>>("TemporaryBackgroundDataWorkspace", "",
Direction::Input, PropertyMode::Optional),
"An (optional) input MDHistoWorkspace used to accumulate background from "
"multiple background MDEventWorkspaces. If unspecified but "
"BackgroundWorkspace is specified, a blank "
"MDHistoWorkspace will be created.");
declareProperty(std::make_unique<WorkspaceProperty<IMDHistoWorkspace>>("TemporaryBackgroundNormalizationWorkspace",
"", Direction::Input, PropertyMode::Optional),
"An (optional) input MDHistoWorkspace used to accumulate background normalization "
"from multiple background MDEventWorkspaces. If unspecified but "
"BackgroundWorkspace is specified, a blank "
"MDHistoWorkspace will be created.");
setPropertyGroup("TemporaryDataWorkspace", "Temporary workspaces");
setPropertyGroup("TemporaryNormalizationWorkspace", "Temporary workspaces");
setPropertyGroup("TemporaryBackgroundDataWorkspace", "Temporary workspaces");
setPropertyGroup("TemporaryBackgroundNormalizationWorkspace", "Temporary workspaces");
declareProperty(std::make_unique<WorkspaceProperty<API::Workspace>>("OutputWorkspace", "", Kernel::Direction::Output),
"A name for the normalized output MDHistoWorkspace.");
declareProperty(
std::make_unique<WorkspaceProperty<API::Workspace>>("OutputDataWorkspace", "", Kernel::Direction::Output),
"A name for the output data MDHistoWorkspace.");
declareProperty(std::make_unique<WorkspaceProperty<Workspace>>("OutputNormalizationWorkspace", "", Direction::Output),
"A name for the output normalization MDHistoWorkspace.");
declareProperty(std::make_unique<WorkspaceProperty<API::Workspace>>(
"OutputBackgroundDataWorkspace", "", Kernel::Direction::Output, PropertyMode::Optional),
"A name for the optional output background data MDHistoWorkspace.");
declareProperty(std::make_unique<WorkspaceProperty<Workspace>>("OutputBackgroundNormalizationWorkspace", "",
Direction::Output, PropertyMode::Optional),
"A name for the optional output background normalization MDHistoWorkspace.");
}
//----------------------------------------------------------------------------------------------
/// Validate the input workspace @see Algorithm::validateInputs
std::map<std::string, std::string> MDNorm::validateInputs() {
std::map<std::string, std::string> errorMessage;
// Check for input workspace frame
Mantid::API::IMDEventWorkspace_sptr inputWS = this->getProperty("InputWorkspace");
if (inputWS->getNumDims() < 3) {
errorMessage.emplace("InputWorkspace", "The input workspace must be at least 3D");
} else {
for (size_t i = 0; i < 3; i++) {
if (inputWS->getDimension(i)->getMDFrame().name() != Mantid::Geometry::QSample::QSampleName) {
errorMessage.emplace("InputWorkspace", "The input workspace must be in Q_sample");
}
}
}
// Optional background input IMDE
Mantid::API::IMDEventWorkspace_sptr bkgdWS = this->getProperty("BackgroundWorkspace");
if (bkgdWS) {
if (bkgdWS->getNumDims() < 3) {
// must have at least 3 dimensions
errorMessage.emplace("BackgroundWorkspace", "The input background workspace must be at least 3D");
} else {
// Check first 3 dimension for Q lab,
for (size_t i = 0; i < 3; i++) {
if (bkgdWS->getDimension(i)->getMDFrame().name() != Mantid::Geometry::QLab::QLabName) {
errorMessage.emplace("BackgroundWorkspace", "The input backgound workspace must be in Q_lab");
}
}
// Check 4th dimension if input workspace is elastic
if (inputWS->getNumDims() > 3) {
if (bkgdWS->getNumDims() <= 3) {
errorMessage.emplace("BackgroundWorkspace", "The input background workspace must have at 4 dimensions when "
"input workspace has more than 4 dimensions (inelastic case).");
} else if (bkgdWS->getDimension(3)->getName() != inputWS->getDimension(3)->getName()) {
errorMessage.emplace("BackgroundWorkspace", "The input background workspace 4th dimension must be DeltaE "
"for inelastic case.");
}
}
}
}
// Check if the vanadium is available for diffraction
bool diffraction = true;
if ((inputWS->getNumDims() > 3) && (inputWS->getDimension(3)->getName() == "DeltaE")) {
diffraction = false;
}
if (diffraction) {
API::MatrixWorkspace_const_sptr solidAngleWS = getProperty("SolidAngleWorkspace");
API::MatrixWorkspace_const_sptr fluxWS = getProperty("FluxWorkspace");
if (solidAngleWS == nullptr) {
errorMessage.emplace("SolidAngleWorkspace", "SolidAngleWorkspace is required for diffraction");
}
if (fluxWS == nullptr) {
errorMessage.emplace("FluxWorkspace", "FluxWorkspace is required for diffraction");
}
}
// Check for property MDNorm_low and MDNorm_high
size_t nExperimentInfos = inputWS->getNumExperimentInfo();
if (nExperimentInfos == 0) {
errorMessage.emplace("InputWorkspace", "There must be at least one experiment info");
} else {
for (size_t iExpInfo = 0; iExpInfo < nExperimentInfos; iExpInfo++) {
auto ¤tExptInfo = *(inputWS->getExperimentInfo(static_cast<uint16_t>(iExpInfo)));
if (!currentExptInfo.run().hasProperty("MDNorm_low")) {
errorMessage.emplace("InputWorkspace", "Missing MDNorm_low log. Please "
"use CropWorkspaceForMDNorm "
"before converting to MD");
}
if (!currentExptInfo.run().hasProperty("MDNorm_high")) {
errorMessage.emplace("InputWorkspace", "Missing MDNorm_high log. Please use "
"CropWorkspaceForMDNorm before converting to MD");
}
}
}
// check projections and UB
if (getProperty("RLU")) {
DblMatrix W = DblMatrix(3, 3);
std::vector<double> Q0Basis = getProperty("QDimension0");
std::vector<double> Q1Basis = getProperty("QDimension1");
std::vector<double> Q2Basis = getProperty("QDimension2");
W.setColumn(0, Q0Basis);
W.setColumn(1, Q1Basis);
W.setColumn(2, Q2Basis);
if (fabs(W.determinant()) < 1e-5) {
errorMessage.emplace("QDimension0", "The projection dimensions are coplanar or zero");
errorMessage.emplace("QDimension1", "The projection dimensions are coplanar or zero");
errorMessage.emplace("QDimension2", "The projection dimensions are coplanar or zero");
}
if (!inputWS->getExperimentInfo(0)->sample().hasOrientedLattice()) {
errorMessage.emplace("InputWorkspace", "There is no oriented lattice "
"associated with the input workspace. "
"Use SetUB algorithm");
}
}
// check dimension names
std::vector<std::string> originalDimensionNames;
for (size_t i = 3; i < inputWS->getNumDims(); i++) {
originalDimensionNames.emplace_back(inputWS->getDimension(i)->getName());
}
originalDimensionNames.emplace_back("QDimension0");
originalDimensionNames.emplace_back("QDimension1");
originalDimensionNames.emplace_back("QDimension2");
std::vector<std::string> selectedDimensions;
for (std::size_t i = 0; i < 6; i++) {
std::string propName = "Dimension" + Strings::toString(i) + "Name";
std::string dimName = getProperty(propName);
std::string binningName = "Dimension" + Strings::toString(i) + "Binning";
std::vector<double> binning = getProperty(binningName);
if (!dimName.empty()) {
auto it = std::find(originalDimensionNames.begin(), originalDimensionNames.end(), dimName);
if (it == originalDimensionNames.end()) {
errorMessage.emplace(propName, "Name '" + dimName +
"' is not one of the "
"original workspace names or a directional dimension");
} else {
// make sure dimension is unique
auto itSel = std::find(selectedDimensions.begin(), selectedDimensions.end(), dimName);
if (itSel == selectedDimensions.end()) {
selectedDimensions.emplace_back(dimName);
} else {
errorMessage.emplace(propName, "Name '" + dimName + "' was already selected");
}
}
} else {
if (!binning.empty()) {
errorMessage.emplace(binningName, "There should be no binning if the dimension name is empty");
}
}
}
// since Q dimensions can be non - orthogonal, all must be present
if ((std::find(selectedDimensions.begin(), selectedDimensions.end(), "QDimension0") == selectedDimensions.end()) ||
(std::find(selectedDimensions.begin(), selectedDimensions.end(), "QDimension1") == selectedDimensions.end()) ||
(std::find(selectedDimensions.begin(), selectedDimensions.end(), "QDimension2") == selectedDimensions.end())) {
for (std::size_t i = 0; i < 6; i++) {
std::string propName = "Dimension" + Strings::toString(i) + "Name";
errorMessage.emplace(propName, "All of QDimension0, QDimension1, QDimension2 must be present");
}
}
// symmetry operations
std::string symOps = this->getProperty("SymmetryOperations");
if (!symOps.empty()) {
bool isSpaceGroup = Geometry::SpaceGroupFactory::Instance().isSubscribed(symOps);
bool isPointGroup = Geometry::PointGroupFactory::Instance().isSubscribed(symOps);
if (!isSpaceGroup && !isPointGroup) {
try {
Geometry::SymmetryOperationFactory::Instance().createSymOps(symOps);
} catch (const Mantid::Kernel::Exception::ParseError &) {
errorMessage.emplace("SymmetryOperations", "The input is not a space group, a point group, "
"or a list of symmetry operations");
}
}
}
// validate accumulation workspaces, if provided
std::shared_ptr<IMDHistoWorkspace> tempNormWS = this->getProperty("TemporaryNormalizationWorkspace");
Mantid::API::IMDHistoWorkspace_sptr tempDataWS = this->getProperty("TemporaryDataWorkspace");
// check that either both or neuther accumulation workspaces are provied
if ((tempNormWS && !tempDataWS) || (!tempNormWS && tempDataWS)) {
errorMessage.emplace("TemporaryDataWorkspace", "Must provide either no accumulation workspaces or,"
"both TemporaryNormalizationWorkspaces and TemporaryDataWorkspace");
}
// check that both accumulation workspaces are on the same grid
if (tempNormWS && tempDataWS) {
size_t numNormDims = tempNormWS->getNumDims();
size_t numDataDims = tempDataWS->getNumDims();
if (numNormDims == numDataDims) {
for (size_t i = 0; i < numNormDims; i++) {
const auto dim1 = tempNormWS->getDimension(i);
const auto dim2 = tempDataWS->getDimension(i);
if ((dim1->getMinimum() != dim2->getMinimum()) || (dim1->getMaximum() != dim2->getMaximum()) ||
(dim1->getNBins() != dim2->getNBins()) || (dim1->getName() != dim2->getName())) {
errorMessage.emplace("TemporaryDataWorkspace", "Binning for TemporaryNormalizationWorkspaces "
"and TemporaryDataWorkspace must be the same.");
break;
}
}
} else { // accumulation workspaces have different number of dimensions
errorMessage.emplace("TemporaryDataWorkspace", "TemporaryNormalizationWorkspace and TemporaryDataWorkspace "
"do not have the same number of dimensions");
}
}
// validate accumulated background workspaces
Mantid::API::IMDHistoWorkspace_sptr tempBkgdDataWS = this->getProperty("TemporaryBackgroundDataWorkspace");
Mantid::API::IMDHistoWorkspace_sptr tempBkgdNormWS = this->getProperty("TemporaryBackgroundNormalizationWorkspace");
// check existing criteria: Background, TempBackgroundData and
// TempBackgroundNormalization must be specified
if (tempBkgdDataWS && (!bkgdWS || !tempDataWS || !tempBkgdNormWS)) {
errorMessage.emplace("TemporaryBackgroundDataWorkspace", "TemporaryBackgroundDataWorkspace is specified but at "
"least one of these is not.");
} else if (tempBkgdNormWS && (!bkgdWS || !tempNormWS || !tempBkgdDataWS)) {
errorMessage.emplace("TemporaryBackgroundNormalizationWorkspace", "TemporaryBackgroundNormalizationWorkspace is "
"specified but at least one of these is not.");
} else if (bkgdWS && tempDataWS && !tempBkgdDataWS) {
errorMessage.emplace("TemporaryDataWorkspace",
"With Background is specifed and TemporaryDataWorkspace is specifed, "
"TemporaryBackgroundDataWorkspace must be specified.");
} else if (tempBkgdDataWS && tempNormWS) {
// check when they both exist
size_t numBkgdDataDims = tempBkgdDataWS->getNumDims();
size_t numBkgdNormDims = tempBkgdNormWS->getNumDims();
size_t numDataDims = tempDataWS->getNumDims();
if (numBkgdDataDims == numBkgdNormDims && numBkgdDataDims == numDataDims) {
// On each dimension, compare min, max, NBins and name
for (size_t idim = 0; idim < numBkgdDataDims; ++idim) {
const auto dimB = tempBkgdDataWS->getDimension(idim);
const auto dimN = tempBkgdNormWS->getDimension(idim);
const auto dimD = tempDataWS->getDimension(idim);
if ((dimB->getMinimum() != dimN->getMinimum()) || (dimB->getMinimum() != dimD->getMinimum()) ||
(dimB->getMaximum() != dimN->getMaximum()) || (dimB->getMaximum() != dimD->getMaximum()) ||
(dimB->getNBins() != dimN->getNBins()) || (dimB->getNBins() != dimD->getNBins()) ||
(dimB->getName() != dimN->getName()) || (dimB->getName() != dimD->getName())) {
errorMessage.emplace("TemporaryBackgroundDataWorkspace",
"TemporaryBackgroundDataWorkspace, "
"TemporaryBackgroundNormalizationWorkspace and "
"TemporaryDataWorkspace "
"must have same minimum, maximum, number of bins and name.");
break;
}
}
} else {
errorMessage.emplace("TemporaryBackgroundDataWorkspace", "TemporaryBackgroundDataWorkspace, "
"TemporaryBackgroundNormalizationWorkspace and "
"TemporaryDataWorkspace must have same dimensions");
}
}
return errorMessage;
}
//----------------------------------------------------------------------------------------------
/** Execute the algorithm.
*/
void MDNorm::exec() {
convention = Kernel::ConfigService::Instance().getString("Q.convention");
// symmetry operations
std::string symOps = this->getProperty("SymmetryOperations");
std::vector<Geometry::SymmetryOperation> symmetryOps;
if (symOps.empty()) {
symOps = "x,y,z";
}
if (Geometry::SpaceGroupFactory::Instance().isSubscribed(symOps)) {
auto spaceGroup = Geometry::SpaceGroupFactory::Instance().createSpaceGroup(symOps);
auto pointGroup = spaceGroup->getPointGroup();
symmetryOps = pointGroup->getSymmetryOperations();
} else if (Geometry::PointGroupFactory::Instance().isSubscribed(symOps)) {
auto pointGroup = Geometry::PointGroupFactory::Instance().createPointGroup(symOps);
symmetryOps = pointGroup->getSymmetryOperations();
} else {
symmetryOps = Geometry::SymmetryOperationFactory::Instance().createSymOps(symOps);
}
g_log.debug() << "Symmetry operations\n";
for (auto so : symmetryOps) {
g_log.debug() << so.identifier() << "\n";
}
m_numSymmOps = symmetryOps.size();
m_isRLU = getProperty("RLU");
// get the workspaces
m_inputWS = this->getProperty("InputWorkspace");
const auto &exptInfoZero = *(m_inputWS->getExperimentInfo(0));
auto source = exptInfoZero.getInstrument()->getSource();
auto sample = exptInfoZero.getInstrument()->getSample();
if (source == nullptr || sample == nullptr) {
throw Kernel::Exception::InstrumentDefinitionError(
"Instrument not sufficiently defined: failed to get source and/or "
"sample");
}
m_samplePos = sample->getPos();
m_beamDir = normalize(m_samplePos - source->getPos());
if ((m_inputWS->getNumDims() > 3) && (m_inputWS->getDimension(3)->getName() == "DeltaE")) {
// DeltaE in input MDE: it cannot be diffraction!
m_diffraction = false;
if (exptInfoZero.run().hasProperty("Ei")) {
Kernel::Property *eiprop = exptInfoZero.run().getProperty("Ei");
m_Ei = boost::lexical_cast<double>(eiprop->value());
if (m_Ei <= 0) {
throw std::invalid_argument("Ei stored in the workspace is not positive");
}
} else {
throw std::invalid_argument("Could not find Ei value in the workspace.");
}
}
// Calculate (BinMD) input sample MDE to MDH and create noramlization MDH from
// it
auto outputDataWS = binInputWS(symmetryOps);
createNormalizationWS(*outputDataWS);
this->setProperty("OutputNormalizationWorkspace", m_normWS);
this->setProperty("OutputDataWorkspace", outputDataWS);
// Background
m_backgroundWS = this->getProperty("BackgroundWorkspace");
DataObjects::MDHistoWorkspace_sptr outputBackgroundDataWS(nullptr);
// Outputs for background related
if (m_backgroundWS) {
outputBackgroundDataWS = binBackgroundWS(symmetryOps);
createBackgroundNormalizationWS(*outputBackgroundDataWS);
this->setProperty("OutputBackgroundNormalizationWorkspace", m_bkgdNormWS);
this->setProperty("OutputBackgroundDataWorkspace", outputBackgroundDataWS);
}
m_numExptInfos = outputDataWS->getNumExperimentInfo();
// loop over all experiment infos
for (uint16_t expInfoIndex = 0; expInfoIndex < m_numExptInfos; expInfoIndex++) {
// Check for other dimensions if we could measure anything in the original
// data
bool skipNormalization = false;
const std::vector<coord_t> otherValues = getValuesFromOtherDimensions(skipNormalization, expInfoIndex);
cacheDimensionXValues();
if (!skipNormalization) {
size_t symmOpsIndex = 0;
for (const auto &so : symmetryOps) {
calculateNormalization(otherValues, so, expInfoIndex, symmOpsIndex);
symmOpsIndex++;
}
} else {
g_log.warning("Binning limits are outside the limits of the MDWorkspace. "
"Not applying normalization.");
}
// if more than one experiment info, keep accumulating
m_accumulate = true;
}
API::IMDWorkspace_sptr out(nullptr);
if (m_backgroundWS) {
// Normalize binned (BinMD) sample workspace with background
out = divideMD(outputDataWS, m_normWS, getPropertyValue("OutputWorkspace"), 0.97, 0.98);
// Normalize background
const std::string normedBkgdWSName("_normedBkgd");
API::IMDWorkspace_sptr outbkgd = divideMD(outputBackgroundDataWS, m_bkgdNormWS, normedBkgdWSName, 0.98, 0.99);
// Clean workspace
auto minusMD = createChildAlgorithm("MinusMD", 0.99, 1.00);
// set up
minusMD->setProperty("LHSWorkspace", out);
minusMD->setProperty("RHSWorkspace", outbkgd);
minusMD->setPropertyValue("OutputWorkspace", getPropertyValue("OutputWorkspace"));
// run and return
minusMD->executeAsChildAlg();
out = minusMD->getProperty("OutputWorkspace");
} else {
// Normalize binned (BinMD) sample workspace without background
out = divideMD(outputDataWS, m_normWS, getPropertyValue("OutputWorkspace"), 0.97, 1.);
}
// Set output workspace
this->setProperty("OutputWorkspace", out);
}
inline API::IMDWorkspace_sptr MDNorm::divideMD(const API::IMDHistoWorkspace_sptr &lhs,
const API::IMDHistoWorkspace_sptr &rhs, const std::string &outputwsname,
const double &startProgress, const double &endProgress) {
auto divideMD = createChildAlgorithm("DivideMD", startProgress, endProgress);
divideMD->setProperty("LHSWorkspace", lhs);
divideMD->setProperty("RHSWorkspace", rhs);
divideMD->setPropertyValue("OutputWorkspace", outputwsname);
divideMD->executeAsChildAlg();
// API::IMDWorkspace_sptr
API::IMDWorkspace_sptr out = divideMD->getProperty("OutputWorkspace");
return out;
}
/**
* Get the dimension name when not using reciprocal lattice units.
* @param i - axis number to return axis name for. Can be 0, 1, or 2.
* @return string containing the name
*/
std::string MDNorm::QDimensionNameQSample(int i) {
if (i == 0)
return std::string("Q_sample_x");
else if (i == 1)
return std::string("Q_sample_y");
else if (i == 2)
return std::string("Q_sample_z");
else
throw std::invalid_argument("Index must be 0, 1, or 2 for QDimensionNameQSample");
}
/**
* Get the dimension name when using reciprocal lattice units.
* @param projection - a vector with 3 elements, containing a
* description of the projection ("1,-1,0" for "[H,-H,0]")
* @return string containing the name
*/
std::string MDNorm::QDimensionName(std::vector<double> projection) {
std::vector<double>::iterator result;
result = std::max_element(projection.begin(), projection.end(), abs_compare);
std::vector<char> symbol{'H', 'K', 'L'};
char character = symbol[std::distance(projection.begin(), result)];
std::stringstream name;
name << "[";
for (size_t i = 0; i < 3; i++) {
if (projection[i] == 0) {
name << "0";
} else if (projection[i] == 1) {
name << character;
} else if (projection[i] == -1) {
name << "-" << character;
} else {
name << std::defaultfloat << std::setprecision(3) << projection[i] << character;
}
if (i != 2) {
name << ",";
}
}
name << "]";
return name.str();
}
/**
* Calculate binning parameters
* @return map of parameters to be passed to BinMD (non axis-aligned)
*/
std::map<std::string, std::string> MDNorm::getBinParameters() {
std::map<std::string, std::string> parameters;
std::stringstream extents;
std::stringstream bins;
std::vector<std::string> originalDimensionNames;
originalDimensionNames.emplace_back("QDimension0");
originalDimensionNames.emplace_back("QDimension1");
originalDimensionNames.emplace_back("QDimension2");
for (size_t i = 3; i < m_inputWS->getNumDims(); i++) {
originalDimensionNames.emplace_back(m_inputWS->getDimension(i)->getName());
}
if (m_isRLU) {
m_Q0Basis = getProperty("QDimension0");
m_Q1Basis = getProperty("QDimension1");
m_Q2Basis = getProperty("QDimension2");
m_UB = m_inputWS->getExperimentInfo(0)->sample().getOrientedLattice().getUB() * 2 * M_PI;
}
std::vector<double> W(m_Q0Basis);
W.insert(W.end(), m_Q1Basis.begin(), m_Q1Basis.end());
W.insert(W.end(), m_Q2Basis.begin(), m_Q2Basis.end());
m_W = DblMatrix(W);
m_W.Transpose();
// Find maximum Q
auto &exptInfo0 = *(m_inputWS->getExperimentInfo(static_cast<uint16_t>(0)));
auto upperLimitsVector =
(*(dynamic_cast<Kernel::PropertyWithValue<std::vector<double>> *>(exptInfo0.getLog("MDNorm_high"))))();
double maxQ;
if (m_diffraction) {
maxQ = 2. * (*std::max_element(upperLimitsVector.begin(), upperLimitsVector.end()));
} else {
double Ei;
double maxDE = *std::max_element(upperLimitsVector.begin(), upperLimitsVector.end());
auto loweLimitsVector =
(*(dynamic_cast<Kernel::PropertyWithValue<std::vector<double>> *>(exptInfo0.getLog("MDNorm_low"))))();
double minDE = *std::min_element(loweLimitsVector.begin(), loweLimitsVector.end());
if (exptInfo0.run().hasProperty("Ei")) {
Kernel::Property *eiprop = exptInfo0.run().getProperty("Ei");
Ei = boost::lexical_cast<double>(eiprop->value());
if (Ei <= 0) {
throw std::invalid_argument("Ei stored in the workspace is not positive");
}
} else {
throw std::invalid_argument("Could not find Ei value in the workspace.");
}
const double energyToK = 8.0 * M_PI * M_PI * PhysicalConstants::NeutronMass * PhysicalConstants::meV * 1e-20 /
(PhysicalConstants::h * PhysicalConstants::h);
double ki = std::sqrt(energyToK * Ei);
double kfmin = std::sqrt(energyToK * (Ei - minDE));
double kfmax = std::sqrt(energyToK * (Ei - maxDE));
maxQ = ki + std::max(kfmin, kfmax);
}
size_t basisVectorIndex = 0;
std::vector<coord_t> transformation;
for (std::size_t i = 0; i < 6; i++) {
std::string propName = "Dimension" + Strings::toString(i) + "Name";
std::string binningName = "Dimension" + Strings::toString(i) + "Binning";
std::string dimName = getProperty(propName);
std::vector<double> binning = getProperty(binningName);
std::string bv = "BasisVector";
if (!dimName.empty()) {
std::string property = bv + Strings::toString(basisVectorIndex);
std::stringstream propertyValue;
propertyValue << dimName;
// get the index in the original workspace
auto dimIndex = std::distance(originalDimensionNames.begin(),
std::find(originalDimensionNames.begin(), originalDimensionNames.end(), dimName));
auto dimension = m_inputWS->getDimension(dimIndex);
propertyValue << "," << dimension->getMDUnits().getUnitLabel().ascii();
for (size_t j = 0; j < originalDimensionNames.size(); j++) {
if (j == static_cast<size_t>(dimIndex)) {
propertyValue << ",1";
transformation.emplace_back(1.f);
} else {
propertyValue << ",0";
transformation.emplace_back(0.f);
}
}
parameters.emplace(property, propertyValue.str());
// get the extents an number of bins
coord_t dimMax = dimension->getMaximum();
coord_t dimMin = dimension->getMinimum();
if (m_isRLU) {
Mantid::Geometry::OrientedLattice ol;
ol.setUB(m_UB * m_W); // note that this is already multiplied by 2Pi
if (dimIndex == 0) {
dimMax = static_cast<coord_t>(ol.a() * maxQ);
dimMin = -dimMax;
} else if (dimIndex == 1) {
dimMax = static_cast<coord_t>(ol.b() * maxQ);
dimMin = -dimMax;
} else if (dimIndex == 2) {
dimMax = static_cast<coord_t>(ol.c() * maxQ);
dimMin = -dimMax;
}
}
if (binning.size() == 0) {
// only one bin, integrating from min to max
extents << dimMin << "," << dimMax << ",";
bins << 1 << ",";
} else if (binning.size() == 2) {
// only one bin, integrating from min to max
extents << binning[0] << "," << binning[1] << ",";
bins << 1 << ",";
} else if (binning.size() == 1) {
auto step = binning[0];
double nsteps = (dimMax - dimMin) / step;
if (nsteps + 1 - std::ceil(nsteps) >= 1e-4) {
nsteps = std::ceil(nsteps);
} else {
nsteps = std::floor(nsteps);
}
bins << static_cast<int>(nsteps) << ",";
extents << dimMin << "," << dimMin + nsteps * step << ",";
} else if (binning.size() == 3) {
dimMin = static_cast<coord_t>(binning[0]);
auto step = binning[1];
dimMax = static_cast<coord_t>(binning[2]);
double nsteps = (dimMax - dimMin) / step;
if (nsteps + 1 - std::ceil(nsteps) >= 1e-4) {
nsteps = std::ceil(nsteps);
} else {
nsteps = std::floor(nsteps);
}
bins << static_cast<int>(nsteps) << ",";
extents << dimMin << "," << dimMin + nsteps * step << ",";
}
basisVectorIndex++;
}
}
parameters.emplace("OutputExtents", extents.str());
parameters.emplace("OutputBins", bins.str());
m_transformation = Mantid::Kernel::Matrix<coord_t>(
transformation, static_cast<size_t>((transformation.size()) / m_inputWS->getNumDims()), m_inputWS->getNumDims());
return parameters;
}
/**
* Create & cached the normalization workspace
* @param dataWS The binned workspace that will be used for the data
*/
void MDNorm::createNormalizationWS(const DataObjects::MDHistoWorkspace &dataWS) {
// Copy the MDHisto workspace, and change signals and errors to 0.
std::shared_ptr<IMDHistoWorkspace> tmp = this->getProperty("TemporaryNormalizationWorkspace");
m_normWS = std::dynamic_pointer_cast<MDHistoWorkspace>(tmp);
if (!m_normWS) {
m_normWS = dataWS.clone();
m_normWS->setTo(0., 0., 0.);
} else {
// Temp is given. Accumulation mode is on
m_accumulate = true;
}
}
void MDNorm::createBackgroundNormalizationWS(const DataObjects::MDHistoWorkspace &bkgdDataWS) {
// requiring background workspace is specified
if (!m_backgroundWS) {
return;
}
// Copy the MDHisto workspace, and change signals and errors to 0.
std::shared_ptr<IMDHistoWorkspace> tmp = this->getProperty("TemporaryBackgroundNormalizationWorkspace");
m_bkgdNormWS = std::dynamic_pointer_cast<MDHistoWorkspace>(tmp);
if (!m_bkgdNormWS) {
m_bkgdNormWS = bkgdDataWS.clone();
m_bkgdNormWS->setTo(0., 0., 0.);
}
}
/**
* Validates the TemporaryDataWorkspace has the same binning
* as the input binning parameters
* @param parameters :: map of binning parameters
* @param tempDataWS :: the workspace weare using to aggregate from
* @return :: bool - true means the binning is correct to aggreagete using
* tempDataWS
*/
void MDNorm::validateBinningForTemporaryDataWorkspace(const std::map<std::string, std::string> ¶meters,
const Mantid::API::IMDHistoWorkspace_sptr &tempDataWS) {
// parse the paramters map and get extents from tempDataWS
const std::string numBinsStr = parameters.at("OutputBins");
const std::string extentsStr = parameters.at("OutputExtents");
const std::vector<size_t> numBins = VectorHelper::splitStringIntoVector<size_t>(numBinsStr);
const std::vector<double> extents = VectorHelper::splitStringIntoVector<double>(extentsStr);
// make sure the number of dimensions is the same for both workspaces
size_t numDimsTemp = tempDataWS->getNumDims();
if ((numBins.size() != numDimsTemp) || (extents.size() != numDimsTemp * 2)) {
std::stringstream errorMessage;
errorMessage << "The number of dimensions in the output and ";
errorMessage << "TemporaryDataWorkspace are not the same.";
throw(std::invalid_argument(errorMessage.str()));
}
// compare the extents and number of bins
for (size_t i = 0; i < numDimsTemp; i++) {
auto ax = tempDataWS->getDimension(i);
if (numBins[i] != ax->getNBins()) {
std::stringstream errorMessage;
errorMessage << "The number of bins output and number of bins in ";
errorMessage << "TemporaryDataWorkspace are not the same along ";
errorMessage << "dimension " << i;
throw(std::invalid_argument(errorMessage.str()));
}
if (std::abs(extents[2 * i] - ax->getMinimum()) > 1.e-5) {
std::stringstream errorMessage;
errorMessage << "The minimum binning value for the output and ";
errorMessage << "TemporaryDataWorkspace are not the same along ";
errorMessage << "dimension " << i;
throw(std::invalid_argument(errorMessage.str()));
}
if (std::abs(extents[2 * i + 1] - ax->getMaximum()) > 1.e-5) {
std::stringstream errorMessage;
errorMessage << "The maximum binning value for the output and ";
errorMessage << "TemporaryDataWorkspace are not the same along ";
errorMessage << "dimension " << i;
throw(std::invalid_argument(errorMessage.str()));
}
}
// sort out which axes are dimensional and check names
size_t parametersIndex = 0;
std::vector<size_t> dimensionIndex(numDimsTemp + 1, 3); // stores h, k, l or Qx, Qy, Qz dimensions
for (auto const &p : parameters) {
auto key = p.first;
auto value = p.second;
// value starts with QDimension0, then other stuff
// do not use ==
if (value.find("QDimension0") != std::string::npos) {
dimensionIndex[0] = parametersIndex;
const std::string dimXName = tempDataWS->getDimension(parametersIndex)->getName();
if (m_isRLU) { // hkl
if (dimXName != QDimensionName(m_Q0Basis)) {
std::stringstream errorMessage;
std::stringstream debugMessage;
errorMessage << "TemporaryDataWorkspace does not have the ";
errorMessage << "correct name for dimension " << parametersIndex;
debugMessage << "QDimension0 Names: Output will be: " << QDimensionName(m_Q0Basis);
debugMessage << " TemporaryDataWorkspace: " << dimXName;
g_log.warning(debugMessage.str());
throw(std::invalid_argument(errorMessage.str()));
}
} else {
if (dimXName != QDimensionNameQSample(0)) {
std::stringstream errorMessage;
std::stringstream debugMessage;
errorMessage << "TemporaryDataWorkspace does not have the ";
errorMessage << "correct name for dimension " << parametersIndex;
debugMessage << "QDimension0 Names: Output will be: " << QDimensionNameQSample(0);
debugMessage << " TemporaryDataWorkspace: " << dimXName;
g_log.warning(debugMessage.str());
throw(std::invalid_argument(errorMessage.str()));
}
}
} else if (value.find("QDimension1") != std::string::npos) {
dimensionIndex[1] = parametersIndex;
const std::string dimYName = tempDataWS->getDimension(parametersIndex)->getName();
if (m_isRLU) { // hkl
if (dimYName != QDimensionName(m_Q1Basis)) {
std::stringstream errorMessage;
std::stringstream debugMessage;
errorMessage << "TemporaryDataWorkspace does not have the ";
errorMessage << "correct name for dimension " << parametersIndex;
debugMessage << "QDimension1 Names: Output will be: " << QDimensionName(m_Q1Basis);
debugMessage << " TemporaryDataWorkspace: " << dimYName;
g_log.warning(debugMessage.str());
throw(std::invalid_argument(errorMessage.str()));
}
} else {
if (dimYName != QDimensionNameQSample(1)) {
std::stringstream errorMessage;
std::stringstream debugMessage;
errorMessage << "TemporaryDataWorkspace does not have the ";
errorMessage << "correct name for dimension " << parametersIndex;
debugMessage << "QDimension1 Names: Output will be: " << QDimensionNameQSample(1);
debugMessage << " TemporaryDataWorkspace: " << dimYName;
g_log.warning(debugMessage.str());
throw(std::invalid_argument(errorMessage.str()));
}
}
} else if (value.find("QDimension2") != std::string::npos) {
dimensionIndex[2] = parametersIndex;
const std::string dimZName = tempDataWS->getDimension(parametersIndex)->getName();
if (m_isRLU) { // hkl
if (dimZName != QDimensionName(m_Q2Basis)) {
std::stringstream errorMessage;
std::stringstream debugMessage;
errorMessage << "TemporaryDataWorkspace does not have the ";
errorMessage << "correct name for dimension " << parametersIndex;
debugMessage << "QDimension2 Names: Output will be: " << QDimensionName(m_Q2Basis);
debugMessage << " TemporaryDataWorkspace: " << dimZName;
g_log.warning(debugMessage.str());
throw(std::invalid_argument(errorMessage.str()));
}
} else {
if (dimZName != QDimensionNameQSample(2)) {
std::stringstream errorMessage;
std::stringstream debugMessage;
errorMessage << "TemporaryDataWorkspace does not have the ";
errorMessage << "correct name for dimension " << parametersIndex;
debugMessage << "QDimension2 Names: Output will be: " << QDimensionNameQSample(2);
debugMessage << " TemporaryDataWorkspace: " << dimZName;
g_log.warning(debugMessage.str());
throw(std::invalid_argument(errorMessage.str()));
}
}
} else if ((key != "OutputBins") && (key != "OutputExtents")) {
// make sure the names of non-directional dimensions are the same
const std::string nameData = tempDataWS->getDimension(parametersIndex)->getName();
if (value.find(nameData) != 0) {
g_log.error() << "Dimension " << nameData
<< " from the temporary workspace"
" is not one of the binning dimensions, "
" or dimensions are in the wrong order."
<< std::endl;
throw(std::invalid_argument("Beside the Q dimensions, "
"TemporaryDataWorkspace does not have the "
"same dimension names as OutputWorkspace."));
}
}
parametersIndex++;
}
const auto it = std::find_if(dimensionIndex.cbegin(), dimensionIndex.cend(),
[numDimsTemp](const auto &idx) { return idx > numDimsTemp; });
if (it != dimensionIndex.cend())
throw(std::invalid_argument("Cannot find at least one of QDimension0, "
"QDimension1, or QDimension2"));
}
/**
* Calculate symmetry operation matrix from Symmetry operation
* @param so :: symmetry operation
* @return :: matrix
*/
inline DblMatrix MDNorm::buildSymmetryMatrix(const Geometry::SymmetryOperation &so) {
// calculate dimensions for binning
DblMatrix soMatrix(3, 3);
auto v = so.transformHKL(V3D(1, 0, 0));
soMatrix.setColumn(0, v);
v = so.transformHKL(V3D(0, 1, 0));
soMatrix.setColumn(1, v);
v = so.transformHKL(V3D(0, 0, 1));
soMatrix.setColumn(2, v);
return soMatrix;
}
// projection: input/output
// requiring: m_hIdx, m_kIndex, m_lIdx, meidx, m_dEintegrated, m_Q0Basis,
// mQ1Basis,
/**
* @brief MDNorm::determineBasisVector
* @param qindex
* @param value
* @param Qtransform
* @param projection
* @param basisVector
* @param qDimensionIndices :: output, Q dimension index mapped to input qindex
*/
inline void MDNorm::determineBasisVector(const size_t &qindex, const std::string &value,
const Mantid::Kernel::DblMatrix &Qtransform, std::vector<double> &projection,